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- PDB-4yoy: Crystal structure of a trimeric exonuclease PhoExo I from Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 4yoy
TitleCrystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dT and Mg2+ ion
Components
  • 3-5 exonuclease PhoExo I
  • 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'
KeywordsHYDROLASE/DNA / exonuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


exonuclease activity / metal ion binding
Similarity search - Function
Protein of unknown function DUF4152 / Protein of unknown function DUF4152 / Protein of unknown function (DUF4152) / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / 3-5 exonuclease PhoExo I
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsMiyazono, K. / Ito, T. / Tanokura, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science, and Technology Japan
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I
Authors: Miyazono, K. / Ishino, S. / Tsutsumi, K. / Ito, T. / Ishino, Y. / Tanokura, M.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-5 exonuclease PhoExo I
B: 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'
C: 3-5 exonuclease PhoExo I
D: 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'
E: 3-5 exonuclease PhoExo I
F: 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9608
Polymers84,9116
Non-polymers492
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-68 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.878, 94.891, 106.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-5 exonuclease PhoExo I


Mass: 26219.281 Da / Num. of mol.: 3 / Mutation: D80N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A060P168
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 2084.392 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.41 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: MES, PEG6000, LiCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→70.836 Å / Num. all: 70614 / Num. obs: 70614 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 31.38 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Rsym value: 0.088 / Net I/av σ(I): 6.454 / Net I/σ(I): 13 / Num. measured all: 494382
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.066.40.8430.964743101810.360.8432.4100
2.06-2.187.40.5431.47177396530.2140.5434.1100
2.18-2.337.40.37826777691090.1490.3785.7100
2.33-2.527.40.2622.96283184660.1030.2627.6100
2.52-2.767.40.1834.15795278540.0720.18310.3100
2.76-3.087.20.10675130470910.0420.10615.7100
3.08-3.566.90.06510.54335863100.0270.06523.7100
3.56-4.366.50.04712.83468253760.020.04731.7100
4.36-6.176.10.04413.82580142140.0190.04434.2100
6.17-19.91160.03914.71416223600.0170.03935.796.8

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementResolution: 1.95→19.911 Å / FOM work R set: 0.825 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 24.53 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2042 6849 5.07 %
Rwork0.1802 128274 -
obs0.1814 70526 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.61 Å2 / Biso mean: 57.69 Å2 / Biso min: 19.9 Å2
Refinement stepCycle: final / Resolution: 1.95→19.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5328 240 2 236 5806
Biso mean--78.76 48.32 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085685
X-RAY DIFFRACTIONf_angle_d1.137727
X-RAY DIFFRACTIONf_chiral_restr0.05886
X-RAY DIFFRACTIONf_plane_restr0.006937
X-RAY DIFFRACTIONf_dihedral_angle_d12.7062174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-1.97210.38052050.380642394444
1.9721-1.99530.4222170.333142404457
1.9953-2.01960.31642520.308943204572
2.0196-2.04520.28542230.288142924515
2.0452-2.07210.30192640.265842104474
2.0721-2.10040.27752280.265343044532
2.1004-2.13040.27462390.255642524491
2.1304-2.16220.29032300.239942964526
2.1622-2.19590.23612220.227742994521
2.1959-2.23190.24332370.208142314468
2.2319-2.27030.23312650.208842284493
2.2703-2.31150.28262500.213143224572
2.3115-2.35590.22552140.20142664480
2.3559-2.40390.24392280.198142494477
2.4039-2.45610.22481840.194343254509
2.4561-2.51310.19331930.191142644457
2.5131-2.57580.22212540.187643084562
2.5758-2.64530.20812270.205642974524
2.6453-2.7230.26542270.198342854512
2.723-2.81060.25421980.191242724470
2.8106-2.91080.21552200.1943094529
2.9108-3.0270.22862300.189442674497
3.027-3.16420.23472560.19342994555
3.1642-3.33030.18132130.179842434456
3.3303-3.53790.2032070.172643294536
3.5379-3.80930.17372230.153542654488
3.8093-4.18940.16122200.143442754495
4.1894-4.78820.13552220.125742844506
4.7882-6.00510.17652370.141942644501
6.0051-19.9120.15272640.146542404504
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.82922.43452.00186.14370.3962.6384-0.11280.19240.68030.0199-0.07610.2784-0.3202-0.18450.1870.19780.04580.02240.35040.03870.320718.13829.77114.4331
25.94310.24110.34861.7122-0.23691.21460.03560.11970.38370.0439-0.0140.1421-0.1631-0.2311-0.04110.2120.0163-0.02930.27260.00110.296714.34127.28026.9281
35.8401-1.2557-1.08154.03762.14776.11730.0760.5170.5656-0.04260.0265-0.2033-0.56180.2278-0.09280.1912-0.0443-0.06180.24060.02880.344134.757830.76179.2715
42.50811.32851.66629.3433-1.94352.0502-0.334-1.51032.29261.45110.12540.71490.1663-0.61470.06880.45960.0512-0.01850.6359-0.19430.829717.754432.931216.269
52.8670.14520.67445.3554-4.36297.70980.0216-0.3855-0.03710.94160.0632-0.2283-0.4136-0.0415-0.07460.3927-0.0026-0.12780.2125-0.02920.396243.12423.932132.9259
64.63960.7454-0.76927.120.76255.48380.0654-0.50750.28630.9152-0.12330.4253-0.1681-0.3330.02770.4417-0.0061-0.07120.2576-0.05350.482537.212839.939433.7423
71.9643-0.95060.27173.8592-1.03022.20630.0007-0.2-0.23550.35560.033-0.27120.16570.1504-0.01640.3147-0.0105-0.11250.20520.02410.412943.489913.153828.7772
87.93450.99790.2075.7496-2.3246.70870.5216-0.86781.88851.218-0.32110.7193-1.5255-1.1837-0.12220.95750.05680.07520.6512-0.08650.839431.478124.839636.8489
91.70990.3964-0.02192.4103-0.421.11740.3593-0.6054-1.06930.25640.22030.42460.5071-0.7231-0.45540.5196-0.1861-0.0190.5430.25030.720617.21891.17728.0161
103.40320.23682.34571.6339-0.39523.0671-0.0089-0.85070.01240.23570.23950.74240.1931-1.4252-0.33250.6176-0.3701-0.00711.00760.40991.19116.4257-1.113629.6721
114.86032.02840.27446.3031-1.44585.76720.354-1.00770.1160.8659-0.26210.88870.1466-1.0916-0.09510.6431-0.16470.13091.00150.18510.636415.26925.860943.4504
123.47762.5196-1.19693.43780.15895.0790.5022-1.07350.19790.9903-0.22791.09350.1433-1.3057-0.29040.9128-0.2140.29261.5130.04730.76519.4746.924347.3499
133.23830.51120.49322.1639-0.72632.01180.1943-0.0567-0.85650.04160.07310.16870.7726-0.3712-0.17460.525-0.1629-0.11310.36830.13290.693119.0925-0.813122.6538
146.60591.4376-0.81472.72082.42367.68690.20950.0102-0.7494-0.15820.16230.02360.8728-0.5119-0.33360.3496-0.0895-0.10220.33470.0560.566413.12395.310611.857
155.32571.87294.81416.1932-0.71445.3913-0.1869-0.74320.67791.0250.46470.9885-0.9361-2.5068-0.30520.70020.08690.20560.89460.16160.869410.187212.060129.3854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 213 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 229 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 11 )B0
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 55 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 56 through 138 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 139 through 229 )C0
8X-RAY DIFFRACTION8chain 'D' and (resid 8 through 11 )D0
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 38 )E0
10X-RAY DIFFRACTION10chain 'E' and (resid 39 through 56 )E0
11X-RAY DIFFRACTION11chain 'E' and (resid 57 through 102 )E0
12X-RAY DIFFRACTION12chain 'E' and (resid 103 through 127 )E0
13X-RAY DIFFRACTION13chain 'E' and (resid 128 through 207 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 208 through 227 )E0
15X-RAY DIFFRACTION15chain 'F' and (resid 8 through 11 )F0

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